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linking problem with modified DNA base

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  • Christian Biertuempfel
    Dear all, I am refining a crystal structure with a modified DNA base. I tried to input the modification via a patch in cns (1.2). So, I modified generate.inp,
    Message 1 of 2 , Jan 26, 2010
      Dear all,
      I am refining a crystal structure with a modified DNA base. I tried to
      input the modification via a patch in cns (1.2). So, I modified
      generate.inp, dna-rna.top, dna-rna.param and dna-rna.link accordingly
      (see below). When I generate pdb/mtf files and refine in cns I do not
      get any errors in the logs. However, all residues of the DNA have broken
      bonds between P and O3' (distance is 1.8 instead of 1.6 A; everywhere
      not only where the modified base is). Can anybody point me to settings I
      can check or things I might have overlooked? Is the link definition correct?

      Of course, I am also trying to define the modification with a
      non-standard residue but a patch would be the easiest solution for my case.

      Thank you,
      christian


      >> in generate.inp:

      patch PCH
      reference=1=(segid A and resid 6)
      reference=2=(segid A and resid 7)
      end

      >> in dna-rna.top:

      PRESidue PCH
      GROUp
      MODIFY ATOM ... TYPE=... END
      ADD BOND ...
      ADD ANGLe ...
      ADD DIHEdral ...
      ADD IMPRoper ...
      END {PCH}

      >> in dna-rna.param

      bond ...
      angle ...
      dihedral ...
      improper ...
      nonbonded ...

      >> in dna-rna.link:

      link nuc head - pch tail + * end
      link pch head - nuc tail + * end


      _______________________________________________________________________

      Dr. Christian Biertümpfel
      Laboratory of Molecular Biology

      NIDDK/National Institutes of Health phone: +1 301 402 4647
      9000 Rockville Pike, Bldg. 5, Rm. B1-03 fax: +1 301 496 0201
      Bethesda, MD 20892-0580
      USA
      _______________________________________________________________________
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